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Mutant Information

SOS indicates the sequenced line is sterile and seeds from siblings are available.

Mutant Name	FN1465-S [Download]
Generation	M2-SOS
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1465-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 43

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 4953868 C-T Homo INTERGENIC
SBS Chr1 15322560 T-A Hetero INTRON
SBS Chr1 15352309 C-G Hetero INTERGENIC
SBS Chr1 15400439 G-A Hetero INTERGENIC
SBS Chr1 25423943 G-T Hetero INTERGENIC
SBS Chr1 25423944 C-T Hetero INTERGENIC
SBS Chr1 26813867 A-G Hetero INTRON
SBS Chr1 34471178 A-T Homo INTERGENIC
SBS Chr2 5555539 T-A Hetero INTERGENIC
SBS Chr2 19403730 A-G Hetero INTERGENIC
SBS Chr2 27282562 G-A Hetero INTERGENIC
SBS Chr3 8964619 A-G Hetero INTERGENIC
SBS Chr3 13442822 A-C Homo INTERGENIC
SBS Chr3 16403869 C-T Hetero INTERGENIC
SBS Chr3 29579708 A-C Homo INTERGENIC
SBS Chr3 34122082 T-C Homo NON_SYNONYMOUS_CODING OsKitaake03g368700
SBS Chr3 35379925 T-C Homo INTERGENIC
SBS Chr4 6171948 T-C Hetero INTERGENIC
SBS Chr4 6869666 G-A Hetero INTERGENIC
SBS Chr4 27755404 T-C Hetero INTRON
SBS Chr5 5819290 G-A Hetero INTERGENIC
SBS Chr5 7752104 G-A Hetero INTERGENIC
SBS Chr5 15898554 G-A Hetero INTERGENIC
SBS Chr5 19635997 C-T Hetero INTERGENIC
SBS Chr5 21154150 T-G Hetero INTERGENIC
SBS Chr5 29834937 G-A Hetero INTERGENIC
SBS Chr6 14301077 C-T Hetero INTERGENIC
SBS Chr6 23285807 C-T Hetero INTERGENIC
SBS Chr7 553109 T-C Hetero INTERGENIC
SBS Chr8 2314451 T-A Homo INTRON
SBS Chr8 11687795 C-A Hetero SPLICE_SITE_DONOR OsKitaake08g102800
SBS Chr9 8614788 C-A Hetero INTERGENIC
SBS Chr9 9726756 G-C Hetero INTERGENIC
SBS Chr9 13069883 C-T Hetero INTERGENIC
SBS Chr9 14064974 G-A Hetero INTERGENIC
SBS Chr9 20979017 G-A Hetero INTRON
SBS Chr10 6878319 A-G Hetero INTERGENIC
SBS Chr10 13367755 T-A Hetero INTERGENIC
SBS Chr10 22778346 C-G Hetero INTERGENIC
SBS Chr11 6458576 A-G Hetero INTERGENIC
SBS Chr12 13986437 C-A Hetero INTERGENIC
SBS Chr12 14032270 T-C Hetero INTERGENIC
SBS Chr12 19264756 C-G Hetero INTERGENIC

Deletions: 27

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr5 309280 309285 5
Deletion Chr1 2860870 2860875 5
Deletion Chr12 3583163 3583164 1
Deletion Chr5 7774908 7774916 8
Deletion Chr6 10039269 10039270 1
Deletion Chr10 10485001 10501000 15999 OsKitaake10g061300
Deletion Chr1 11107876 11107877 1
Deletion Chr9 13859772 13859773 1
Deletion Chr9 14236001 14251000 14999 OsKitaake09g095800
Deletion Chr4 15780001 15788000 7999 OsKitaake04g077400
Deletion Chr6 15959689 15959692 3
Deletion Chr2 16310001 16322000 11999 OsKitaake02g167700
Deletion Chr12 16710501 16710516 15
Deletion Chr4 17669001 17715000 45999 2
Deletion Chr4 17722892 17722893 1
Deletion Chr6 17906001 17916000 9999 OsKitaake06g164800
Deletion Chr12 18802001 18960000 157999 8
Deletion Chr9 19022396 19022397 1 OsKitaake09g152500
Deletion Chr5 22049001 22059000 9999 OsKitaake05g179900
Deletion Chr9 22339001 22351000 11999 OsKitaake09g202500
Deletion Chr2 23429427 23429436 9 OsKitaake02g229500
Deletion Chr7 27677001 27688000 10999 OsKitaake07g258500
Deletion Chr6 28541001 28549000 7999 2
Deletion Chr6 29195001 29206000 10999 3
Deletion Chr1 32289450 32289453 3
Deletion Chr1 34704869 34704880 11
Deletion Chr3 37622254 37622265 11

Insertions: 4

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr1 8610634 8610637 2
Insertion Chr2 17642860 17642863 2 OsKitaake02g176900
Insertion Chr10 10029022 10029025 2
Insertion Chr9 19991864 19991867 2 OsKitaake09g166800

Inversions: 4

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr4 15438181 16153553
Inversion Chr12 18803610 19265258
Inversion Chr4 27080274 27155271 OsKitaake04g197600
Inversion Chr4 27080455 27155285 OsKitaake04g197600

Translocations: 9

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr9 10346253 Chr4 17596731
Translocation Chr9 10346392 Chr4 19196424 OsKitaake04g097300
Translocation Chr12 18956782 Chr7 4087348 OsKitaake07g051900
Translocation Chr9 21415852 Chr1 39729363 OsKitaake09g186500
Translocation Chr9 21416002 Chr1 39729359 OsKitaake09g186500
Translocation Chr9 21416003 Chr7 10640331 OsKitaake09g186500
Translocation Chr9 21417374 Chr7 10640325 OsKitaake09g186600
Translocation Chr4 27080284 Chr3 25149601 OsKitaake03g266400
Translocation Chr4 27080428 Chr3 25149597 OsKitaake03g266400

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	4953868	C-T	Homo	INTERGENIC
SBS	Chr1	15322560	T-A	Hetero	INTRON
SBS	Chr1	15352309	C-G	Hetero	INTERGENIC
SBS	Chr1	15400439	G-A	Hetero	INTERGENIC
SBS	Chr1	25423943	G-T	Hetero	INTERGENIC
SBS	Chr1	25423944	C-T	Hetero	INTERGENIC
SBS	Chr1	26813867	A-G	Hetero	INTRON
SBS	Chr1	34471178	A-T	Homo	INTERGENIC
SBS	Chr2	5555539	T-A	Hetero	INTERGENIC
SBS	Chr2	19403730	A-G	Hetero	INTERGENIC
SBS	Chr2	27282562	G-A	Hetero	INTERGENIC
SBS	Chr3	8964619	A-G	Hetero	INTERGENIC
SBS	Chr3	13442822	A-C	Homo	INTERGENIC
SBS	Chr3	16403869	C-T	Hetero	INTERGENIC
SBS	Chr3	29579708	A-C	Homo	INTERGENIC
SBS	Chr3	34122082	T-C	Homo	NON_SYNONYMOUS_CODING	OsKitaake03g368700
SBS	Chr3	35379925	T-C	Homo	INTERGENIC
SBS	Chr4	6171948	T-C	Hetero	INTERGENIC
SBS	Chr4	6869666	G-A	Hetero	INTERGENIC
SBS	Chr4	27755404	T-C	Hetero	INTRON
SBS	Chr5	5819290	G-A	Hetero	INTERGENIC
SBS	Chr5	7752104	G-A	Hetero	INTERGENIC
SBS	Chr5	15898554	G-A	Hetero	INTERGENIC
SBS	Chr5	19635997	C-T	Hetero	INTERGENIC
SBS	Chr5	21154150	T-G	Hetero	INTERGENIC
SBS	Chr5	29834937	G-A	Hetero	INTERGENIC
SBS	Chr6	14301077	C-T	Hetero	INTERGENIC
SBS	Chr6	23285807	C-T	Hetero	INTERGENIC
SBS	Chr7	553109	T-C	Hetero	INTERGENIC
SBS	Chr8	2314451	T-A	Homo	INTRON
SBS	Chr8	11687795	C-A	Hetero	SPLICE_SITE_DONOR	OsKitaake08g102800
SBS	Chr9	8614788	C-A	Hetero	INTERGENIC
SBS	Chr9	9726756	G-C	Hetero	INTERGENIC
SBS	Chr9	13069883	C-T	Hetero	INTERGENIC
SBS	Chr9	14064974	G-A	Hetero	INTERGENIC
SBS	Chr9	20979017	G-A	Hetero	INTRON
SBS	Chr10	6878319	A-G	Hetero	INTERGENIC
SBS	Chr10	13367755	T-A	Hetero	INTERGENIC
SBS	Chr10	22778346	C-G	Hetero	INTERGENIC
SBS	Chr11	6458576	A-G	Hetero	INTERGENIC
SBS	Chr12	13986437	C-A	Hetero	INTERGENIC
SBS	Chr12	14032270	T-C	Hetero	INTERGENIC
SBS	Chr12	19264756	C-G	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr5	309280	309285	5
Deletion	Chr1	2860870	2860875	5
Deletion	Chr12	3583163	3583164	1
Deletion	Chr5	7774908	7774916	8
Deletion	Chr6	10039269	10039270	1
Deletion	Chr10	10485001	10501000	15999	OsKitaake10g061300
Deletion	Chr1	11107876	11107877	1
Deletion	Chr9	13859772	13859773	1
Deletion	Chr9	14236001	14251000	14999	OsKitaake09g095800
Deletion	Chr4	15780001	15788000	7999	OsKitaake04g077400
Deletion	Chr6	15959689	15959692	3
Deletion	Chr2	16310001	16322000	11999	OsKitaake02g167700
Deletion	Chr12	16710501	16710516	15
Deletion	Chr4	17669001	17715000	45999	2
Deletion	Chr4	17722892	17722893	1
Deletion	Chr6	17906001	17916000	9999	OsKitaake06g164800
Deletion	Chr12	18802001	18960000	157999	8
Deletion	Chr9	19022396	19022397	1	OsKitaake09g152500
Deletion	Chr5	22049001	22059000	9999	OsKitaake05g179900
Deletion	Chr9	22339001	22351000	11999	OsKitaake09g202500
Deletion	Chr2	23429427	23429436	9	OsKitaake02g229500
Deletion	Chr7	27677001	27688000	10999	OsKitaake07g258500
Deletion	Chr6	28541001	28549000	7999	2
Deletion	Chr6	29195001	29206000	10999	3
Deletion	Chr1	32289450	32289453	3
Deletion	Chr1	34704869	34704880	11
Deletion	Chr3	37622254	37622265	11

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr4	15438181	16153553
Inversion	Chr12	18803610	19265258
Inversion	Chr4	27080274	27155271	OsKitaake04g197600
Inversion	Chr4	27080455	27155285	OsKitaake04g197600

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Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes